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Sample GSM1064520 Query DataSets for GSM1064520
Status Public on Feb 04, 2013
Title HU_WT_RNAseq_rep2
Sample type SRA
 
Source name Splenic B Cells
Organism Mus musculus
Characteristics cell type: In vitro activated B Cells
strain: 129/Sv x C57BL/6
genotype: wildtype
growth duration: 28 hr
treatment protocol: 10 mM hydroxyurea for 6 hrs
Growth protocol CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) for 28 hrs.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Ambion) following manufacturer's protocol. RNA was washed, purified using RNeasy kit (Qiagen), and measured for quality. RNA was then prepared for sequencing using the TruSeq RNA sample prep kit (Illumina). Four libraries were sequenced on one lane of HiSeq 2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
Genome_build: mm9
RNA-Seq sequenced reads were mapped to mm9 using Tophat v2.0.6. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using exons of each transcript annotated by BioConductor's GenomicFeatures 1.10.1.
 
Submission date Jan 15, 2013
Last update date May 15, 2019
Contact name Robert Babak Faryabi
E-mail(s) [email protected]
Phone 215-573-8220
Organization name University of Pennsylvania
Department Pathology
Lab Faryabi Lab
Street address Room 553 BRB II/III, 421 Curie Boulevard
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL13112
Series (1)
GSE43504 Genome-wide mapping of early replication fragile sites (ERFS)
Relations
SRA SRX217136
BioSample SAMN01886668

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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